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@dogversioning dogversioning released this 04 Apr 12:54
· 75 commits to main since this release
v2.0.0
5ce8d77
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Learn about vigilant mode.

Breaking changes:

  • Table columns renamed to better match FHIR names
  • Overhaul of how codings are handled - now dynamically detected and joined as appropriate
  • All core tables are strictly 2 dimensional; unnesting should not be required if using core as the basis.
  • Minimum python version is now 3.10

Other major changes:

  • Core builds :should: now gracefully react to missing nested data from the EHR
    • magical string cumulus_none added to reflect cases where null data was recieved from a downstream system
  • Added missing required/must support fields from US Core R4
  • Overhaul of template infrastructure to better centralize/reuse code
  • Added duckdb support, which we are now using for unit tests
  • Propensity score matching added as an available statistical library

Minor changes:

  • Schema validation is now more robustly case insensitive
  • Added additional coding fields to the discovery study
  • Added --archive cli command for storing study data outside athena
  • Added --generate-sql cli command for making example output from a study's jinja templates
  • Added --generate-md cli command to create markdown documentation directly from a database
  • Switched to ruff for linting/security
  • id field is now always the first column in a FHIR resource table
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